Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites

Hunter L Gage,Catherine J Merrick

doi:10.1186/s12864-020-6625-x

Abstract

BackgroundThe Plasmodium genus of malaria parasites encodes several families of antigen-encoding genes. These genes tend to be hyper-variable, highly recombinogenic and variantly expressed. The best-characterized family is the var genes, exclusively found in the Laveranian subgenus of malaria parasites infecting humans and great apes. Var genes encode major virulence factors involved in immune evasion and the maintenance of chronic infections. In the human parasite P. falciparum, var gene recombination and diversification appear to be promoted by G-quadruplex (G4) DNA motifs, which are strongly associated with var genes in P. falciparum. Here, we investigated how this association might have evolved across Plasmodium species – both Laverania and also more distantly related species which lack vars but encode other, more ancient variant gene families.ResultsThe association between var genes and G4-forming motifs was conserved across Laverania, spanning ~ 1 million years of evolutionary time, with suggestive evidence for evolution of the association occurring within this subgenus. In rodent malaria species, G4-forming motifs were somewhat associated with pir genes, but this was not conserved in the Laverania, nor did we find a strong association of these motifs with any gene family in a second outgroup of avian malaria parasites. Secondly, we compared two different G4 prediction algorithms in their performance on extremely A/T-rich Plasmodium genomes, and also compared these predictions with experimental data from G4-seq, a DNA sequencing method for identifying G4-forming motifs. We found a surprising lack of concordance between the two algorithms and also between the algorithms and G4-seq data.ConclusionsG4-forming motifs are uniquely strongly associated with Plasmodium var genes, suggesting a particular role for G4s in recombination and diversification of these genes. Secondly, in the A/T-rich genomes of Plasmodium species, the choice of prediction algorithm may be particularly influential when studying G4s in these important protozoan pathogens.

Highlights

The Plasmodium genus of malaria parasites encodes several families of antigen-encoding genes
G-quadruplex-forming motifs in all Laveranian genomes are associated with var genes In the P. falciparum genome, a search for putative quadruplex-forming sequences (PQSs) using QGRS Mapper was published in 2016, finding 80 Putative quadruplex sequence (PQS), of which 35 were var-associated [23]
We repeated the search for PQSs in all members of the Laveranian subgenus, including P. falciparum, using two PQS prediction tools, QGRS Mapper and G4 Hunter (Fig. 2a)

Summary

Introduction

The Plasmodium genus of malaria parasites encodes several families of antigen-encoding genes. Gage and Merrick BMC Genomics (2020) 21:236 These capacities have been linked, in several species, to the variant expression of virulence factors that are exposed on the infected erythrocyte surface and are encoded by highly variable families of variantly-expressed virulence genes. Such gene families are best-characterized in P. falciparum, where the var gene family encodes ~ 60 variants of P. falciparum Erythrocyte Membrane Protein 1 (PfEMP1) [2,3,4], an adhesin which allows infected erythrocytes to adhere to the vascular endothelium and avoid splenic clearance. Var genes are restricted to the Laveranian subgenus of Plasmodium, which infects great apes and includes the human-infecting P. falciparum species [5], but other Plasmodium species encode other gene families that may have similar roles, including the sicavar family in the macaque parasite P. knowlesi [6, 7] and the pir family which appears widely in many species from rodent to human malarias [8, 9] (Fig. 1)

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